Re: [NMusers] Rcpp alongside NONMEM

From: Itziar Irurzun Arana <itzirurzun_at_alumni.unav.es>
Date: Thu, 3 Nov 2016 18:48:49 +0100

Hi Mike,

I had the same problem some months ago and what I finally did was to update
the path environment variable for the current R session only with the
following code:

    path <- "C:\\RBuildTools" #Write the path to your Rtools or RBuildTools
folder
    rtools <- paste(path, "\\bin", sep = "")
    gcc <- paste(path, "\\gcc-4.6.3\\bin", sep = "")
    path <- strsplit(Sys.getenv("PATH"), ";")[[1]]
    new_path <- c(rtools, gcc, path)
    new_path <- new_path[!duplicated(tolower(new_path))]
    Sys.setenv(PATH = paste(new_path, collapse = ";"))


I always run this before using simulation tools which rely on Rcpp and it
works. When you close your R session this information is lost, so you
wouldn't have problems with other compilers. Then you can leave the NONMEM
gfortran compiler in the first place on the PATH.

If you have more questions, don't hesitate to ask.

Itziar Irurzun

2016-11-03 17:42 GMT+01:00 Smith, Mike K <mike.k.smith_at_pfizer.com>:

> Hi,
>
>
>
> My colleagues and I are running into problems using modelling and
> simulation tools which rely on Rcpp (e.g. Stan, mrgsolve, PKPDsim)
> alongside an existing NONMEM installation. The problem is that we have TW=
O
> versions of compilers installed – one for NONMEM and one from the=
 Rtools
> set.
>
>
>
> For NONMEM we’re using gfortran 4.5.0 installed in C:\Program Fil=
es
> (x86)\gfortran\libexec\gcc\i586-pc-mingw32\4.5.0. (Running Windows 8).
>
>
>
> When Rtools installs it allows me to configure where the RBuildTools sit=
s
> on the PATH, but if I put it first (as recommended) then it stops NONMEM
> picking up the gfortran compiler above, and NONMEM doesn’t run
> successfully. But if I put the RBuildTools further down the path, then it
> doesn’t set up c++ as a command line executable.
>
>
>
> If anyone has experience at making these play nicely together without
> having to hack the PATH, I’d be really interested to hear from yo=
u. While
> hacking PATH variables is fine individually, it’s not a recipe th=
at’s
> easily rolled out and supported across an organisation… (Although=
 I’d still
> like to know how you might hack the PATH info to get this to work!).
>
>
>
> M
>
> *Mike K. Smith*
> *Pharmacometrics*
>
> *Pfizer WRD, Sandwich** (IPC 096)*
> Tel: +44 (0)1304 643561
>
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>



--

Itziar Irurzun Arana, PhD Student
Department of Pharmacy and Pharmaceutical Technology
School of Pharmacy, University of Navarra
Pamplona, Spain

Received on Thu Nov 03 2016 - 13:48:49 EDT

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